Accelerating chemical database searching using graphics processing units

Journal of Chemical Information and Modeling

Volumn 51, Issue 8, 2011, Pages 1807-1816

  Liu, Pu ^a   Agrafiotis, Dimitris K ^a   Rassokhin, Dmitrii N ^a   Yang, Eric ^a  

^a JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION THEORY; COMPUTER GRAPHICS; DATABASE SYSTEMS; INFORMATION RETRIEVAL; MOLECULES; PROGRAM PROCESSORS; QUERY PROCESSING; SEARCH ENGINES;

CHEMICAL DATABASE; COMPRESSION ALGORITHMS; COMPUTATIONAL BURDEN; FINGERPRINT VECTOR; ORDERS OF MAGNITUDE; RETRIEVAL PERFORMANCE; STORAGE AND RETRIEVALS; STRUCTURAL FEATURE;

GRAPHICS PROCESSING UNIT;

ORGANIC COMPOUND;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER PROGRAM; DATA MINING; FACTUAL DATABASE; INFORMATION PROCESSING; METHODOLOGY; STATISTICS;

ALGORITHMS; CHEMISTRY, PHARMACEUTICAL; COMPUTER GRAPHICS; DATA COMPRESSION; DATA MINING; DATABASES, FACTUAL; MODELS, CHEMICAL; MOLECULAR STRUCTURE; ORGANIC CHEMICALS; SOFTWARE;

EID: 80051992077     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200164g     Document Type: Article

References (34)

1. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors; Wiley-VCH: Weinheim, Germany and New York, 2002.
2. Durant, J. L.; Leland, B. A.; Henry, D. R.; Nourse, J. G. Reoptimization of MDL Keys for Use in Drug Discovery J. Chem. Inf. Comput. Sci. 2002, 46, 1273-1280 (Pubitemid 35468313)
3. McGregor, M. J.; Pallai, P. V. Clustering of Large Databases of Compounds: Using the MDL "Keys" as Structural Descriptors J. Chem. Inf. Comput. Sci. 1997, 37, 443-448 (Pubitemid 127603548)
4. Barnard, J. M.; Downs, G. M. Chemical Fragment Generation and Clustering Software J. Chem. Inf. Comput. Sci. 1997, 37, 141-142
5. Baldi, P.; Benz, R. W.; Hirschberg, D. S.; Swamidass, S. J. Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval J. Chem. Inf. Model. 2007, 47, 2098-2109 (Pubitemid 350275076)
6. Bolton, E.; Wang, Y.; Thiessen, P. A.; Bryant, S. H. PubChem: Integrated Platform of Small Molecules and Biological Activities. In Annual Reports in Computational Chemistry; American Chemical Society: Washington, DC, USA, 2008; Vol. 4, pp 217-241.
7. Satish, N.; Harris, M.; Garland, M. Designing Efficient Sorting Algorithms for Manycore GPUs. Proceedings of the 2009 IEEE International Symposium on Parallel and Distributed Processing; IEEE Computer Society: Washington, DC, USA, 2009; pp 1-10.
8. Suchard, M. A.; Wang, Q.; Chan, C.; Frelinger, J.; Cron, A.; West, M. Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures J. Comput. Graph. Stat. 2010, 19, 419-438
9. Liu, C. cuHMM: A CUDA Implementation of Hidden Markov Model Training and Classication. http://code.google.com/p/chmm (accessed Feb 12, 2011).
10. Do, T.-N.; Nguyen, V.-H. A; Novel Speed-up, S. V. M. Algorithm for Massive Classification Tasks. Proceedings of RIVF'2008; IEEE Press:: Ho Chi Minh, Vietnam, 2008; pp 215-220.
11. Catanzaro, B.; Sundaram, N.; Keutzer, K. Fast Support Vector Machine Training and Classification on Graphics Processors. In ICML'08: Proceedings of 25th International Conference on Machine Learning; Cohen, W. W.; McCallum, A.; Roweis, S., Eds. ACM Press: New York, NY, and Helsinki, Finland, 2008; pp 104-111.
12. Liao, Q.; Wang, J.; Webster, Y.; Watson, I. A. GPU Accelerated Support Vector Machines for Mining High-Throughput Screening Data J. Chem. Inf. Model. 2009, 49, 2718-2725
13. Lieberman, M. D.; Sankaranarayanan, J.; Samet, H. A Fast Similarity Join Algorithm Using Graphics Processing Units. Proceedings of the 2008 IEEE 24th International Conference on Data Engineering; IEEE Computer Society: Washington, DC, USA, 2008; pp 1111-1120.
14. Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. Accelerating Molecular Dynamic Simulation on Graphics Processing Units J. Comput. Chem. 2009, 30, 864-872
15. Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L. G.; Schulten, K. Accelerating Molecular Modeling Applications with Graphics Processors J. Comput. Chem. 2007, 28, 2618-2640 (Pubitemid 350074136)
16. Stivala, A. D.; Stuckey, P. J.; Wirth, A. I. Fast and Accurate Protein Substructure Searching with Simulated Annealing and GPUs BMC Bioinf. 2010, 11, 446
17. Haque, I. S.; Pande, V. S. PAPER-Accelerating Parallel Evaluations of ROCS J. Comput. Chem. 2009, 31, 117-132
18. Haque, I. S.; Pande, V. S.; Walters, W. P. SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs J. Chem. Inf. Model. 2010, 50, 560-564
19. Rogers, D.; Hahn, M. Extended-Connectivity Fingerprints J. Chem. Inf. Model. 2010, 50, 742-754
20. Bender, A.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C. K.; Glick, M.; Davies, J. W. How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space J. Chem. Inf. Model. 2009, 49, 108-119
21. Golomb, S. W. Run-length Encodings IEEE Trans. Inf. Theory 1965, 12, 399-401
22. Elias, P. Universal Codeword Sets and Representations of the Integers IEEE Trans. Inf. Theory 1975, 21, 194-203
23. Tsuchiyama, R.; Nakamura, T.; Lizuka, T.; Asahara, A. The OpenCL Programming Book; Fixstars: Oakland, CA, 2010.
24. NVIDIA CUDA C Programming Guide 3.2; NVidia: Santa Clara, CA, 2010.
25. Karimi, K.; Dickson, N. G.; Hamze, F. A Performance Comparison of CUDA and OpenCL. arXiv.org, 2010; Vol. abs/1005.2581.
26. Xu, H.; Agrafiotis, D. K. Nearest Neighbor Search in General Metric Spaces Using a Tree Data Structure with a Simple Heuristic J. Chem. Inf. Model. 2003, 43, 1933-1941
27. Lipkus, A. H. A. Proof of the Triangle Inequality for the Tanimoto Distance J. Math. Chem. 1999, 26, 263-265
28. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of Topological Descriptors for Similarity-Based Virtual Screening Using Multiple Bioactive Reference Structures Org. Biomol. Chem 2004, 2, 3256-3266
29. Liu, R.; Zhou, D. Using Molecular Fingerprint as Descriptors in the QSPR Study of Lipophilicity J. Chem. Inf. Model. 2008, 48, 542-549 (Pubitemid 351535422)
30. Swamidass, S. J.; Baldi, P. Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time J. Chem. Inf. Model. 2007, 47, 302-317 (Pubitemid 46615935)
31. Swamidass, S. J.; Chen, J.; Bruand, J.; Phung, P.; Ralaivola, L.; Baldi, P. Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity Bioinformatics 2005, 21, i359-368
32. Agrafiotis, D. K.; Lobanov, V. S.; Salemme, F. R. Combinatorial Informatics in the Post-genomics Era Nat. Rev. Drug Discovery 2002, 1, 337-346 (Pubitemid 37361463)
33. Agrafiotis, D. K.; Alex, S.; Dai, H.; Derkinderen, A.; Farnum, M.; Gates, P.; Izrailev, S.; Jaeger, E. P.; Konstant, P.; Leung, A.; Lobanov, V. S.; Marichal, P.; Martin, D.; Rassokhin, D. N.; Shemanarev, M.; Skalkin, A.; Stong, J.; Tabruyn, T.; Vermeiren, M.; Wan, J.; Xu, X. Y.; Yao, X. Advanced Biological and Chemical Discovery (ABCD): Centralizing Discovery Knowledge in an Inherently Decentralized World J. Chem. Inf. Model. 2007, 47, 1999-2014 (Pubitemid 350275069)
34. Golovin, A.; Henrick, K. Chemical Substructure Search in SQL J. Chem. Inf. Model. 2009, 49, 22-27